Post-transcriptional Gene Regulation in Stem Cells 

We are broadly interested in post-transcriptional gene regulation and its role in stem cell biology and in cancer development. Our current focus is on the mRNA 3′ end processing and its regulation. We combine biochemical, structural, and high throughput sequencing-based global analyses in our research.

The 3′ ends of most eukaryotic mRNAs are formed by an endonucleolytic cleavage and the subsequent addition of a string of adenosines. Interestingly, the transcripts of ~70% of genes in all eukaryotes have alternative 3′ ends that are formed by cleavage/polyadenylation at different sites, a phenomenon called mRNA alternative polyadenylation (APA). APA not only expands the proteomic and functional diversity, but also plays important roles in gene regulation. Deregulation of mRNA 3′ processing and APA have been implicated in a wide spectrum of human diseases. However, it remains poorly understood how poly(A) sites are recognized and how their recognition is regulated. Our goal is to decipher the rules that govern poly(A) site choice, or the “polyadenylation code”, by using a combination of biochemical, genomic, and genetic approaches. Our studies aim to provide novel insights into the basic mechanisms of post-transcriptional gene regulation as well as its role in many physiological and pathological processes..

  • mRNA APA regulation in stem cells and cancer.

We have recently developed a high throughput sequencing-based method called PAS-seq for quantitatively RNA polyadenylation profiling at the transcriptome level. Using this method, we detected extensive changes in the global APA profile during stem cell differentiation to neurons that, in most cases, lead to 3′ UTR lengthening (Shepard et al., RNA 2011). Recently we have identified the protein Fip1 as a critical regulator of the global APA profile and we have demonstrated that Fip1-mediated APA regulation is essential for embryonic stem cell self-renewal and for somatic reprogramming (Lackford et al., EMBO J 2014). These studies revealed an unexpected role for post-transcriptional gene regulation in stem cell biology. Given the similarities between stem cells and cancer cells, we are also investigating whether and how APA regulation may contribute to cancer development.


Fip1 is essential for embryonic stem cell self-renewal. (Lackford et al., EMBO J. 2014)

  • Characterization of the mRNA 3′ processing machinery.

Previously we have purified the human mRNA 3′ processing complex in its active and intact form (Shi et al., Mol Cell 2009). Surprisingly, this complex consists of more than 85 proteins, including the core 3′ processing factors and many peripheral factors that may couple mRNA 3′ end formation to other cellular processes. To understand how the mRNA 3′ processing machinery recognizes specific poly(A) sites, we have systematically studied the key protein-RNA interactions for the core mRNA 3′ processing factors (Yao et al., PNAS 2012; Yao et al., RNA 2013; Chan et al. Genes & Dev 2014). Our most recent study (Chan et al. Genes & Dev 2014) has significantly reshaped the 20-year old model for poly(A) site recognition.

Electron microscopy images of purified human mRNA 3′ processing complex (Shi et al., Mol Cell 2009)

Our research is funded by: